Abstract: Aneuploidy is a common feature of many congenital disorders such as Down?s Syndrome, or Trisomy21. It is an extremely common feature in cancer, and nearly all solid tumors and almost half of hematopoetic cancers are aneuploid. The current gold standard for assessment of aneugen activity is the micronucleus assay. We are developing a novel molecular assay for aneuploidy using single cell RNA sequencing (scRNAseq). The assay will indicate whether a cell is euploid or aneuploid, which chromosome(s) affected, and how a toxicant has affected the target cell transcriptome, either independent of or in conjunction with one or more aneuploid chromosomes. Elucidation of the affected or predictive pathways, gene families and cellular processes will provide a rich, highly detailed global view of the consequences of compound exposure on a cell, and may lead to a molecular understanding of different fates for different chromosome aneuploidies.